Rosetta 3.1 Release Manual

Documentation for FloppyTail application

Author:
Steven Lewis smlewi@gmail.com

Metadata

Last edited 2/2/10. Code and documentation by Steven Lewis smlewi@gmail.com.

Examples

The code is at rosetta_source/src/apps/public/scenarios/FloppyTail/; there's an integration test which serves as a demo at rosetta_source/test/integration/tests/FloppyTail/

References

Purpose and Algorithm

This code was written for a relatively singular application. The system in question was a protein with a long (dozens of residues) flexible tail, which was not seen in crystal structures. Biochemical evidence suggested a particular binding site for the tail on a known binding partner (the two binding partners also had a known binding interface separate from this tail). The code was intended to model the reach of the long flexible tail and determine whether the hypothesized binding site was plausible.

The algorithm is fairly simple: small/shear/fragment moves in centroid mode to collapse the tail into some sort of folded conformation from an initially straight-out-into-space extended conformation, and small/shear moves with repacking to refine its position.

This code can also model internally flexible regions between domains, although that is not its intended purpose. It may not do a good job of detecting appropriate interfaces for repacking in this latter case.

The code is compatible with constraints. Early modeling proceeded using constraints and some small hacks to help guide models to the hypothesized tail-binding site. Ultimately this was not necessary for the original system, but the code retains the ability to use constraints, etc. Your mileage may vary.

This code is NOT intended to do "half-abinitio" where you know half a structure and want to fold the other half. Although it is modeled on abinitio, it is only tested on a truly floppy tail, and I have no idea if it is able to fold compact structures.

Input Files

See test/integration/tests/FloppyTail/ for example usage.

Tips

This code was intended for a single purpose, but it may work if you have a similarly flexible tail. It can also model internal flexible regions between domains.

Density-Scoring Options

FloppyTail supports three types of options: general Rosetta 3.x options (packing, etc.), generic protocol options like "how many cycles" borrowed from the AnchoredDesign application (not included in the release), and FloppyTail specific options.

FloppyTail options

AnchoredDesign options (borrowed for simplicity, not tied to AnchoredDesign in any other way); all are in the AnchoredDesign namespace General options: All packing namespace options loaded by the PackerTask are respected. jd2 namespace options are respected. Anything very low-level, like the database paths, is respected.
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